RootscanR (version 0.0.1)

findAvgSurface: Find the average surface level

Description

findAvgSurface - This function looks at several images which should have the same surface level, for example the root scans (topmost depth window) of the same minirhizotron. Then, the best position of the surface level is determined by finding the best across all images.

Usage

findAvgSurface(
  img_paths = NULL,
  imgs = NULL,
  surface_col = "red",
  pos_highpoint_px = "center",
  radius_highpoint_px = 10,
  angle = 45,
  top_side = "left",
  ppcm = NULL,
  ppi = NULL
)

Value

findAvgSurface A list with the two values 'pos_surf_px' and 'depth_highpoint_cm', and a matrix 'all_split_info' containing the information on all possible splits.

Arguments

img_paths

(Optional, default = NULL) Character vector specifying all of the individual image paths of interest. This is only used if imgs is set to NULL.

imgs

List of images (e.g., provided by the RootDetector). Each image can be a PNG, i.e., an array with 3 dimensions (3 layers each containing a 2-dim. numeric matrix with values between 0 and 1), or a 2-dim. matrix.

surface_col

Color of the area to be split of the mask (default "red"). Can be of any of the three kinds of R color specifications, i.e., either a color name (as listed by colors()), a hexadecimal string (see Details), or a positive integer (indicates using palette()).

pos_highpoint_px

Either one of "center" or "edge" (default), indicating that scanning starts at the bottom or top facing side of the minirhizotron, respectively, or it can also be an integer value (>=1 and <=width of the top_side of the image) specifying where (left<->right) in the top row of the image the highest point of the image lies, indicating the column where the minimum points of the depth-level lines lie.
"edge" is equivalent to using 1 or width of the top_side and "center" to using half the width of the top_side.

radius_highpoint_px

The radius specifying how large the are should be to determine the split (default 10).

angle

Numeric value >=0 and <=90 (default 45) specifying the installation angle of the minirhizotron in degrees (angle between the ground and the tube above the soil).

top_side

One of "left","top" (default),"right","bottom". Indicates where the upper side of the image is.

ppcm

Numeric value specifying how many pixels there are per centimeter (resolution of the image). Default NULL. If ppcm is not NULL or NA, ppi is ignored.
Examples: 300 ppi (printing) is 118 ppcm, 150 ppi is 59 ppcm, 72 ppi (screens) is 28 ppcm.

ppi

Numeric value specifying how many pixels there are per inch (resolution of the image). Default NULL. Leave/set ppcm to NULL or NA to use ppi.
Examples: 300 ppi (printing) is 118 ppcm, 150 ppi is 59 ppcm, 72 ppi (screens) is 28 ppcm.

Examples

# Example of finding the best overlap of two sets of two matrices.
mat_R <- matrix(c(1,1,1,1,1,
                  0,1,1,1,1,
                  0,0,1,1,1), ncol = 5, nrow = 3, byrow = TRUE)
mat_G <- matrix(c(0,0,0,0,1,
                  0,1,0,0,1,
                  0,0,1,1,1), ncol = 5, nrow = 3, byrow = TRUE)
mat_G2 <- matrix(c(0,0,0,1,0,
                   0,0,0,0,0,
                   0,0,1,1,1), ncol = 5, nrow = 3, byrow = TRUE)
mat_B <- matrix(c(0,0,0,0,1,
                  0,0,0,0,1,
                  0,0,1,1,1), ncol = 5, nrow = 3, byrow = TRUE)
mat_B2 <- matrix(c(0,0,0,0,0,
                   0,1,0,0,1,
                   0,0,1,1,1), ncol = 5, nrow = 3, byrow = TRUE)
surface <- findAvgSurface(imgs = list(
                  array(c(mat_R,mat_G,mat_B), dim = c(dim(mat_R),3)),
                  array(c(mat_R,mat_G2,mat_B), dim = c(dim(mat_R),3)),
                  array(c(mat_R,mat_G,mat_B2), dim = c(dim(mat_R),3))),
                         radius_highpoint_px = 2, top_side = "top", ppcm = 1)